NEW YORK (CBSNewYork/AP) — Losses are piling, tempers are flaring and players are being benched.

Throw in all the penalties, mistakes and questionable play calling, and the New York Jets have the troubling look and feel of a dysfunctional bunch.

Todd Bowles’ team is 3-6, matching its loss total from last season, and its playoff prospects already appear highly unlikely. The second-year coach, however, doesn’t agree with the increasingly negative perception.

“Not at all,” Bowles said during a conference call Monday. “I know what reality is, so we know what everything is inside this building and we’re a close-knit group.”

But, perhaps the most glaring sign of trouble within came Sunday, when Bowles benched star defensive linemen Muhammad Wilkerson and Sheldon Richardson for the first quarter of New York’s 27-23 loss at Miami .

Bowles repeated Monday that it was “a coach’s decision,” adding that non-injury and non-football issues are kept in-house. He also declined to say whether tardiness is an issue with the two.

However, reports emerged that both Wilkerson and Richardson were disciplined for being late to a team meeting. NJ.com reported that the two have been late or no-showed more than once. NFL Network reported that Wilkerson missed a walkthrough and a defensive meeting at which his birthday was being celebrated — complete with a cake — the day before the game against Baltimore last month. Wilkerson did not play in that game because of an ailing ankle.

“Those are reports,” Bowles said. “Those things are handled in-house and I know how we handle things in here, and everybody is accountable for their actions. We handle things in here as we handle them, and I’m perfectly fine with those two (players’) commitments.”

When asked what makes him satisfied with both Wilkerson and Richardson, Bowles said simply: “They put in work. They put in a lot of work.”

A sideline exchange between wide receiver Brandon Marshall and quarterback Ryan Fitzpatrick appeared to get a bit heated, although both downplayed it after the game. Bowles did the same, brushing aside the notion that it was another example of a team tearing apart.

“We had more turmoil going last year when we won four or five in a row,” Bowles said. “This year is normal. Brandon and Fitz talk on the sideline all the time. That’s just football talk. That goes without saying. And, Mo and Sheldon are fine.”

On Monday, Marshall said it was “business as usual” among the players, with the focus on moving forward to their next game at home against the Los Angeles Rams on Sunday.

He said he feels good about the Jets’ locker room, calling it “one of the best I’ve been in.” He was lukewarm, however, when asked if he thought every player was committed to a common goal.

“You never know,” he said. “It’s the National Football League. There are so many different personalities in the room. I love what Coach (Marc) Trestman said when he first got hired in Chicago, one of his first team meetings, he said: We don’t need all. We just need the right ones.'”

Tackle Ben Ijalana thinks the Jets have those guys, along with the right approach.

“Everyone is focused on trying to right the ship and we’re playing a game at home,” he said. “We’re not trying to lull down. We’re just trying to get back on the right track, continue to get these wins going.”

The Jets are uncertain whether Fitzpatrick will start because of a sprained left knee, and some fans and media says New York should go with second-year quarterback Bryce Petty regardless.

“It’s expected,” Marshall said of the perception that the Jets are a team in chaos. “This is what happens, usually, when you lose. … We’re sitting at 3-6, we’re disappointed in our play, disappointed in ourselves.”

And the players aren’t alone.

Bowles has taken his share of the blame, too, and had missteps in his play calls throughout the season.

“I haven’t done a good job,” he said. “We’re 3-6. It speaks for itself. I can do a lot better job of coaching.”

Despite all that, though, Bowles insisted he has total control of his team.

“Completely, yes,” he said. “I know me and I know how I address the team and I know how the team responds. I have no issues with that.”

Penalties are a big problem, with 10 called in the game against the Dolphins. Perhaps none was as glaring as the offsides call on Antonio Allen, whose mistake on a kickoff resulted in a re-kick — and Kenyan Drake returned it 96 yards for the go-ahead touchdown in the fourth quarter.

“We don’t finish,” Ijalana said. “I would say it’s a combination of not finishing and sometimes starting slow. In this league, those things get you in trouble. It’s very hard to win games like that.”